This thesis demonstrates ways in which the ammonium group can be used to template the formation of rotaxanes, and to control their submolecular motion. The first part details the development of a methodology for synthesising rotaxanes from cyclic peptide macrocycles. Cyclic octa- and deca- peptides of the L-ProGly repeat unit are versatile ionophores that are known to bind both metal ions and organic cations. One mode of binding exhibited by this type of macrocycle is to associate a cation on either face of the macrocycle: a so called ‘sandwich complex’. If the two cations with which the macrocycle binds are secondary ammonium groups connected by a spacer of suitable length, then an inclusion complex is formed. Trapping of this type of inclusion complex by covalent modification has allowed access for the first time to synthetic rotaxanes of cyclic peptides. The latter half of this thesis details the synthesis and operation of two different switchable molecular shuttles in which the position of the macrocycle is determined by a change in the protonation level of the molecule. The first of these shuttles operates by a combination of amide-amide and crown ether-ammonium interactions. In its neutral form these amide-amide hydrogen bonds hold the macrocycle over a dipeptide residue. When an amine group in the thread is protonated, polyether-ammonium cation interactions dominate and the macrocycle changes position. The second shuttle relies solely on crown ether-ammonium interactions. In this instance pH controlled movement is achieved by the selective deprotonation of one of two ammonium stations, inducing the macrocycle to reside predominantly on the second, less acidic, station.